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Mouse C57BL/6NJ (C57BL_6NJ_v3)

Mouse C57BL/6NJ assembly and gene annotation

Assembly

The assembly for C57BL/6NJ was generated as part of The Mouse Genomes Project , additional strains can be found in Ensembl.

The assembly is on the chromosome level, consisting of 798 contigs assembled into 208 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 8304515 while the scaffold N50 is 126851431.

Other assemblies

Gene annotation

Genome annotation was generated by mapping GENCODE M30 genes and transcripts via the Ensembl Human automated annotation system, supplemented by methods from the Ensembl vertebrate annotation pipeline. Mapped GENCODE structures served as the primary evidence with gaps in the annotations filled using aligned short-read transcriptomic data and full-length transcripts derived from PacBio IsoSeq long-read data.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyC57BL_6NJ_v3, INSDC Assembly GCA_921999865.2, Jul 2022
Base Pairs2,514,609,827
Golden Path Length2,514,609,827
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2023
Genebuild released
Genebuild last updated/patchedJun 2023
Database version115.2

Gene counts

Coding genes23,141
Non coding genes16,648
Small non coding genes5,258
Long non coding genes10,829
Misc non coding genes561
Pseudogenes12,383
Gene transcripts109,121